Variant report

Variant	rs769449
Chromosome Location	chr19:45410002-45410003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45408654..45411235-chr19:45491614..45494162,2	MCF-7	breast:
2	chr19:45407734..45410496-chr19:45474972..45477815,2	K562	blood:
3	chr19:45406430..45412448-chr19:45445993..45451546,6	K562	blood:
4	chr19:45409871..45413630-chr19:45417200..45419965,4	MCF-7	breast:
5	chr19:45409844..45412639-chr19:45456918..45459928,3	K562	blood:
6	chr19:45408290..45410344-chr19:45572852..45575175,2	K562	blood:
7	chr19:45405563..45412018-chr19:45456830..45459683,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104853	Chromatin interaction
ENSG00000104859	Chromatin interaction
ENSG00000130208	Chromatin interaction
ENSG00000234906	Chromatin interaction
ENSG00000267114	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10119	0.83[ASN][1000 genomes]
rs10414043	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs429358	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256200	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73052335	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912129	chr19:45379791-45448465	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv912130	chr19:45382034-45448465	Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv912131	chr19:45391582-45415640	Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv912132	chr19:45393473-45415640	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912133	chr19:45395619-45482884	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv912134	chr19:45395619-45528799	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv912135	chr19:45408312-45415640	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv912136	chr19:45408836-45413874	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv912137	chr19:45408836-45415640	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv912138	chr19:45409113-45415640	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Alzheimer's disease biomarkers	23562540	GWAS catalog
C-reactive protein	18439548	GWAS catalog
Cognitive decline (age-related)	24468470	GWAS catalog

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45400400-45414200	Weak transcription	Hela-S3	cervix
2	chr19:45406800-45414200	Weak transcription	Lung	lung
3	chr19:45407800-45410400	Enhancers	Spleen	Spleen
4	chr19:45408000-45410400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:45408400-45410200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:45408600-45410200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr19:45408600-45410200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:45408600-45410200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr19:45408600-45410200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:45408600-45410200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:45408600-45410200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr19:45408600-45410400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:45408600-45410400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr19:45408600-45410400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr19:45408800-45410200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr19:45408800-45410200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:45408800-45410200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
18	chr19:45408800-45410200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
19	chr19:45408800-45410200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:45408800-45410200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr19:45408800-45410200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
22	chr19:45408800-45410200	Flanking Active TSS	K562	blood
23	chr19:45409000-45410200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:45409200-45410200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:45409200-45410200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
26	chr19:45409200-45410400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:45409400-45414200	Weak transcription	Gastric	stomach
28	chr19:45409600-45410200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:45409600-45410400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:45409600-45414200	Weak transcription	HMEC	breast
31	chr19:45409600-45414400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:45409800-45410200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr19:45409800-45410200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:45409800-45410200	Flanking Active TSS	Liver	Liver
35	chr19:45409800-45410200	Flanking Active TSS	HepG2	liver
36	chr19:45409800-45410800	Active TSS	Brain Anterior Caudate	brain
37	chr19:45410000-45410200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr19:45410000-45410200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:45410000-45410200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:45410000-45410200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:45410000-45410200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr19:45410000-45410200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr19:45410000-45410200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:45410000-45410200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:45410000-45410200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:45410000-45410200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:45410000-45410200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
48	chr19:45410000-45410200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
49	chr19:45410000-45410200	Enhancers	Duodenum Mucosa	Duodenum
50	chr19:45410000-45410200	Flanking Active TSS	Fetal Intestine Large	intestine

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